CAlerts are now three years old and come from a Bitcoin that was much less stable than it is now. I see the ability to send and display long custom strings to the user as a security threat. This old CAlert system was over looked and I apologise for that. Going forward we will have a much less intrusive way of informing users of an updated client. The idea is that a client will connect to a JSON feed to see if there is a higher number, if it is it will the user to upgrade and if it is not or it cannot find the site it will remain quiet. There will be no ability to display custom strings.
Bushstar, why do you think that a centralized solution is better than using the dencentralized message system that is part of Bitcoin already? Having a centralized server for checking for upgrades is bad due to possible ddos and having the server hacked. The alert system works well and is really the only way for me to contact old clients. Some Litecoin users are running 0.5 and aren't on the forums. So there's really no other way for them to be notified of a critical update otherwise. By disabling the alert system without a replacement in place, you are shooting yourself in the foot if in the future you want to contact these clients of a critical security flaw.
It's true that there is a threat of the alert key being leaked and anyone can then send messages to all the clients. But if you look at the code, you will see that satoshi has thought of this already like everything else he's done. You can send a max priority alert that's hardcoded to tell everyone that the alert key has been compromised and that everyone should upgrade. And this alert will override any other alerts.